Following the American Revolution, the waterfront site was used to build merchant vessels. Federal authorities purchased the old docks and 40 acres (160,000 m2) of land for forty thousand dollars in 1801, and the property became an active U.S. Navyshipyard five years later, in 1806. The offices, store-houses and barracks were constructed of handmade bricks, and the yard's oldest structure (located in Vinegar Hill), the 1807 federal style commandant's house, was designed by Charles Bulfinch, architect of the United States Capitol in Washington, D.C.. Many officers were housed in Admiral's Row.

The nation's first ironclad ship, Monitor, was fitted with its revolutionary iron cladding at the Continental Iron Works in nearby Greenpoint. By the American Civil War, the yard had expanded to employ about 6000 men. In 1890, the ill-fated Maine was launched from the Yard's ways.

On the eve of World War II, the yard contained more than five miles (8 km) of paved streets, four drydocks[1] ranging in length from 326 to 700 feet (99 to 213 meters), two steel shipways, and six pontoons and cylindrical floats for salvage work, barracks for marines, a power plant, a large radio station, and a railroad spur, as well as the expected foundries, machine shops, and warehouses. In 1937 the battleshipNorth Carolina was laid down. In 1938, the yard employed about ten thousand men, of whom one-third were Works Progress Administration (WPA) workers. The battleship Iowa was completed in 1942 followed by the Missouri which became the site of the Surrender of Japan 2 September 1945. On 12 January 1953, test operations began on Antietam, which emerged in December 1952 from the yard as America's first angled-deck aircraft carrier.

At its peak, during World War II, the yard employed 70,000 people, 24 hours a day.

During World War II, the pedestrian walkways on the Williamsburg and Manhattan Bridges spanning the East River offered a good overhead view of the navy yard, and were therefore encased in order to prevent espionage.

The Brooklyn Naval Hospital, constructed 1830–1838 and rebuilt 1841–1843, was decommissioned in the mid-1970s.[2][3][4] It was one of the oldest naval hospitals in the United States. The 60,000 square foot complex was designed by Martin E. Thompson. The hospital had its beginning in 1825 when the Secretary of the Navy purchased 25 acres adjacent to the Brooklyn Naval Yard. The hospital was active between the Civil War through World War II with the Navy Surgeon General reporting in 1864 an average of 229 patients, with 2,135 treated during the year. The hospital also counted on its staff some of first female nurses and medical students in the United States Navy.

Rumors of the shipyard's closure came two years before the shipyard closed in 1966. Seymour Melmen, an engineering economist at the Columbia University Graduate School of Engineering, looked into the plight of the shipyard workers at the N.Y.N.S. and came up with a detailed plan for converting the then New York Naval Ship Yard into a commercial shipyard which could have saved most of the skilled shipyard jobs. The plan was never put in place. The Wagner Administration looked to the auto industry to build a car plant inside the Yard. No U.S. car manufacturer was interested and foreign car manufacturers claimed that with the conversion of the dollar, it was too expensive. The Navy decommissioned the yard in 1966, after the completion of the Austin-classamphibious transport dockUSS Duluth. The Johnson Administration refused to sell the yard to the City of New York for 18 months. When the new Nixon Administration came into power they signed the papers to sell the yard to the city. Leases were signed inside the yard even before the sale of the yard to the City was signed.

Base housing at Ryerson Avenue gate

In 1967, Seatrain Shipbuilding, which was wholly owned by Seatrain Lines, signed a lease with the Commerce Labor Industry Corporation of Kings (CLICK) which was established as a non-profit body to run the yard for the city. CLICK's lease with the newly formed Seatrain Shipbuilding was not very business friendly. Seatrain planned to build five Very Large Crude Carriers (VLCC's) and seven container ships for Seatrain Lines. It eventually built four VLCCs (the largest ships ever to be built in the Brooklyn Navy Yard), eight barges and one ice-breaker barge. The last ship to be built in the Brooklyn Navy Yard was the VLCC Bay Ridge, built by Seatrain Shipbuilding. In 1977 the Bay Ridge was converted from a VLCC to a FPSOV [Floating Production Storage Offtake Vessel]. The Bay Ridge was renamed Kuito and is operating for Chevron off of the Coast of Angola in 400 meters of water in the Kuito oil field.[5] The year 1976 would bring peak employment inside the yard with nearly 6,000 workers with Seatrain Shipbuilding and Coastal Dry Dock & Repair accounting for 80% of the employment.

In 1979, Seatrain Lines closed its gates, ending the history of Brooklyn shipbuilding. In 1972 Coastal Dry Dock & Repair Corp leased the three small dry docks and several buildings inside the yard from CLICK. Coastal Drydock only repaired and converted US Navy vessels but closed in 1987.[6] CLICK had been replaced by the non-profit Brooklyn Navy Yard Development Corporation in 1981. By 1987, the Brooklyn Navy Yard Development Corporation failed in all attempts to lease any of the six dry docks and buildings to any shipbuilding or ship-repair company.

The Yard has become an area of private manufacturing and commercial activity. Today, more than 200 businesses operate at the Yard and employ approximately 5,000 people.[7]Brooklyn Grange Farms operates a 65,000 square feet (6,000 m2) commercial farm on top of Building 3.[8]Steiner Studios is one of the yard's more prominent tenants with one of the largest production studios outside Los Angeles. Many artists also lease space and have established an association called Brooklyn Navy Yard Arts.

The Yard has three piers and a total of 10 berths ranging from 350 to 890 feet (270 m) long, with ten-foot deck height and 25 to 40 feet (7 to 12 meters) of depth alongside. The drydocks are now operated by GMD Shipyard Corp. A federal project maintains a channel depth of 35 feet (10 m) from Throggs Neck to the yard, about two miles (3 km) from the western entrance, and thence 40 feet (12 m) of depth to the deep water in the Upper Bay. Currents in the East River can be strong, and congestion heavy. Access to the piers requires passage under the Manhattan Bridge (a suspension span with a clearance of 134 feet (41 m) and the Brooklyn Bridge (a suspension span with a clearance of 127 feet (39 m).

In November 2011, Brooklyn Navy Yard Center at BLDG 92, a museum dedicated to the yard's history and future, opened its doors.[9][10] A program of the Brooklyn Navy Yard Development Corporation, the Center offers exhibits, public tours, educational programs, archival resources and workforce development services.[11]

The museum's main exhibit focuses on the history of the Navy Yard and its impact on American industry, technology, innovation and manufacturing, as well as national and New York City's labor, politics, education, and urban and environmental planning. There are also displays and videos about the new businesses in the facility.

A bronze marker on the nearby Brooklyn Bridge contains a section commemorating the history of the shipyard, mentioning several of the notable ships that were built there, including Maine, Missouri and the last ship constructed there, Duluth.[15]